Dear Jeremy,
Thanks very much for the report. Timing was bad on my end, and a preliminary
inspection suggested this was going to take some digging. And it did.
Text for the clickable part of a cross-reference was being assumed to be all
text, no HTML elements (very old code, a rookie mistake). So as David suggested
the new "span" alerting MathJax was being built and then dropped. One such
example has always been in the sample article, which nobody had noticed. (Look
now, since it may be a few hours before I update it.)
Worse, *any* formatting in the clickable of a cross-reference was getting
dropped. So, a PreTeXt "em" in a title creates an HTML "span.emphasis" that was
not surving into an "xref" by the title. Sample article now has such an example.
Merged now. Website update soon. Confirmation for your project would be
welcome (perhaps on the next CLI update?). Thanks again.
Rob